Species transport in thin-film Nafion heavily influences proton-exchange membrane (PEMFC) performance, particularly in low-platinum-loaded cells. Literature suggests that phase-segregated nanostructures in hydrated Nafion thin films can reduce species mobility and increase transport losses in cathode catalyst layers. However, these structures have primarily been observed at silicon−Nafion interfaces rather than at more relevant material (e.g., Pt and carbon black) interfaces. In this work, we use neutron reflectometry and X-ray photoelectron spectroscopy to investigate carbon-supported Nafion thin films. Measurements were taken in humidified environments for Nafion thin films (≈30−80 nm) on four different carbon substrates. Results show a variety of interfacial morphologies in carbon-supported Nafion. Differences in carbon samples' roughness, surface chemistry, and hydrophilicity suggest that thin-film Nafion phase segregation is impacted by multiple substrate characteristics. For instance, hydrophilic substrates with smooth surfaces correlate with a high likelihood of lamellar phase segregation parallel to the substrate. When present, the lamellar structures are less pronounced than those observed at silicon oxide interfaces. Local oscillations in water volume fraction for the lamellae were less severe, and the lamellae were thinner and were not observed when the water was removed, all in contrast to Nafion−silicon interfaces. For hydrophobic and rough samples, phase segregation was more isotropic rather than lamellar. Results suggest that Nafion in PEMFC catalyst layers is less influenced by the interface compared with thin films on silicon. Despite this, our results demonstrate that neutron reflectometry measurements of silicon−Nafion interfaces are valuable for PEMFC performance predictions, as water uptake in the majority Nafion layers (i.e., the uniformly hydrated region beyond the lamellar region) trends similarly with thickness, regardless of support material.